RetrogeneDB ID: retro_opri_352

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_686:1124853..1126272(-)
• Located in intron of: ENSOPRG00000012844

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: HYAL2
• Ensembl ID: ENSOPRG00000015387
• Aliases: None
• Description: hyaluronoglucosaminidase 2 [Source:HGNC Symbol;Acc:5321]

Sequence

>retro_opri_352
ATGCAGGTGGGCCCAGGCCCCACCTTCACACTGGCCCTGGTGCTGGCAGTGGCACAGGCCATGGACCTCAAGCCTACAGC
ACCGCCCATTTTCACGGGCCGACCATTTGTGGTGGCCTGGGACGTGCCCACACAGGACTGTGGTCCCCGGCACAAGGTGC
CATTAGACCTGAAGGCCTTCGATGTGCAAGCCTCCCCGAATGAGGGGTTTGTGAACCAGAACATCACCATCTTTTACCAT
GATCGCCTGGGCCCATACCCGCGCTTCGACCTGGCTGGCCACTCAGTGCACGGTGGCGTGCCGCAGAATGGCAGCCTCTG
GGCGCACCTCAAAATGCTGCAGCAGCGAGTAGAACACTACATCCGTTCCCAGGAGCCTCCTGGCCTGGCCGTCATCGACT
GGGAGGACTGGCGGCCCGTGTGGGTGCGCAACTGGCAGGACAAAGACGTGTACCGCCGCTGGTCCCGCCAGCTAGGGGCC
AGTCGGCACCCAGATTGGCCAGCCGACCGCATCGTGAAGCAGGCACAGTATGAGTTCGAGTTCGCCGCTCGCCAGTTCAT
GCTGGAGACGCTACGCTACGTCAAGGCAGTGCGGCCTCGGCACCTCTGGGGCTTCTACCTCTTTCCTGACTACTACAACC
ACGATTACGCGCAGAACCGGGAGAGCTATACAGGCCGCTGCCCGGACGTTGAAGTGGCCCGCAACGACCAGCTGGCCTGG
CTGTGGGCCGAGAGCACGGCCCTCTATCCCTCTGTCTATCTGGACGAGACCCTGGCCTCCTCTGTCCAAGGCCGCAACTT
TGTCAGTTTCCGGGTTCAGGAGGCCCTGAGCGTGGCTCACACCCATCATGCCTCCCATGCACTCCCCGTCTACGTCTTCA
CGCGCCCCACCTACAGTCGCCGACTCACTGGACTCAGCGAGTTGGACCTCATTTCCACCATTGGCGAGAGCGCGGCCCTG
GGTGCAGCCGGGGTCATCCTGTGGGGTGACGCAGGCTACACCACAAGCACGGAGACCTGCCAGTACCTCAAGGATTACCT
GACACAACTGTTGGTCCCATATGTGGTCAACGTGTCCTGGGCCACCCAGTATTGCAGCACGGCCCGGTGCCATGACCATG
GGCGCTGCTTGCATCGCAACCCCAACGCCAATACCTTCTTGCACCTCAGCACTAGCAGCTTCTGCCTAGTGCCTGGCCAT
GAACCTGGCGAGCCCCAGCTGAGACCCGAGGGGTAGCTCAGCAGGGCTGACCTTGACCACCTGCAGAAGCACTTTCGCTG
TCAGTGCTACTTGGGCTGGGGTGGCGAGCAATGCCAGCAAGACAATAGGCAAGTGGCTGGGGGTGCCGTGGAGGCCTGGG
CTGGGTCCTACCTCAGCAGCCTGCTGGCCCTGGCAGTCCTGGTCCTCCCCTGGACCTTG

Alignment

ORF - retro_opri_352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQVGPGPTVTLALVLAVARAMDLKPTAPPIFTGRPFVVAWDVPTQDCGPRHKVPLDLKAFDVQASPNEGF
          MQVGPGPT.TLALVLAVA.AMDLKPTAPPIFTGRPFVVAWDVPTQDCGPRHKVPLDLKAFDVQASPNEGF
Retrocopy MQVGPGPTFTLALVLAVAQAMDLKPTAPPIFTGRPFVVAWDVPTQDCGPRHKVPLDLKAFDVQASPNEGF

Parental  VNQNITIFYHDRLGLYPRFDPAGHSVHGGVPQNGSLWAHLKMLQQRVEHYIRSQEPPGLAVIDWEDWRPV
          VNQNITIFYHDRLG.YPRFD.AGHSVHGGVPQNGSLWAHLKMLQQRVEHYIRSQEPPGLAVIDWEDWRPV
Retrocopy VNQNITIFYHDRLGPYPRFDLAGHSVHGGVPQNGSLWAHLKMLQQRVEHYIRSQEPPGLAVIDWEDWRPV

Parental  WVRNWQDKDVYRRWSRQLVASRHPDWPADRIVKQAQYEFEFAARQFMLETLRYVKAVRPRHLWGFYLFPD
          WVRNWQDKDVYRRWSRQL.ASRHPDWPADRIVKQAQYEFEFAARQFMLETLRYVKAVRPRHLWGFYLFPD
Retrocopy WVRNWQDKDVYRRWSRQLGASRHPDWPADRIVKQAQYEFEFAARQFMLETLRYVKAVRPRHLWGFYLFPD

Parental  CYNHDYAQNRESYTGRCPDVEVARNDQLAWLWAESTALYPSVYLDETLASSVHGRNFVSFRVQEALRVAH
          .YNHDYAQNRESYTGRCPDVEVARNDQLAWLWAESTALYPSVYLDETLASSV.GRNFVSFRVQEAL.VAH
Retrocopy YYNHDYAQNRESYTGRCPDVEVARNDQLAWLWAESTALYPSVYLDETLASSVQGRNFVSFRVQEALSVAH

Parental  THHASHALPVYVFTRPTYSRRLTGLSEMDLISTIGESAALGAAGVILWGDAGYTTSTETCQYLKDYLTQL
          THHASHALPVYVFTRPTYSRRLTGLSE.DLISTIGESAALGAAGVILWGDAGYTTSTETCQYLKDYLTQL
Retrocopy THHASHALPVYVFTRPTYSRRLTGLSELDLISTIGESAALGAAGVILWGDAGYTTSTETCQYLKDYLTQL

Parental  LVPYVVNVSWATQYCSTARCHDHGRCLRRNPNANTFLHLSASSFRLVPGHEPGEPQLRPEGELSRADLDH
          LVPYVVNVSWATQYCSTARCHDHGRCL.RNPNANTFLHLS.SSF.LVPGHEPGEPQLRPEG.LSRADLDH
Retrocopy LVPYVVNVSWATQYCSTARCHDHGRCLHRNPNANTFLHLSTSSFCLVPGHEPGEPQLRPEG*LSRADLDH

Parental  LQKHFRCQCYLGWGGERCQQDNRQVAGGAVESWAGSYLSSLLALAVLVLPWTL
          LQKHFRCQCYLGWGGE.CQQDNRQVAGGAVE.WAGSYLSSLLALAVLVLPWTL
Retrocopy LQKHFRCQCYLGWGGEQCQQDNRQVAGGAVEAWAGSYLSSLLALAVLVLPWTL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_352 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000015387	2 retrocopies	retro_opri_1207, retro_opri_352 ,